Studying the Tumor Immune Microenvironment: How Multi-Omics Is Transforming Cancer Research

Cancer development and progression are influenced not only by genetic alterations within tumor cells, but also by the complex ecosystem surrounding them: the tumor microenvironment (TME). The TME consists of multiple interacting components, including cancer cells, immune cells, stromal cells, endothelial cells, and extracellular matrix components.

Understanding these interactions is essential for studying cancer development. However, no single omics technique can capture the full complexity of cancer biology. This is where multi-omics approaches become valuable, integrating complementary molecular layers to provide a more comprehensive view of tumor evolution, immune regulation, and treatment response.

Figure 1. Multi-omics framework for studying the tumor immune microenvironment.

1. Identifying Tumor-Driving Alterations Through WES/WGS

Cancer begins with genomic alterations that accumulate during tumor development. Human whole-genome sequencing (hWGS) and whole-exome sequencing (WES) enable researchers to characterize the genetic landscape of tumors, particularly when analyzing matched tumor and normal samples.

With these methods, researchers can distinguish inherited germline variants from tumor-specific somatic alterations. This analysis provides insights into:

• Copy number variations (CNVs), loss of heterozygosity (LOH), and genomic instability
• Mutational signatures and mechanisms driving tumor evolution
• Tumor heterogeneity and clonal evolution

Understanding these genomic alterations helps identify potential driver mutations and biomarkers associated with therapy response. Tumor genomic profiles can also reveal mechanisms influencing antitumor immunity, including mutational burden, neoantigen generation, and alterations associated with immune escape.

2. Revealing Regulatory Mechanisms Through Epigenomics

Genomic alterations alone do not explain all changes observed in cancer. Epigenetic mechanisms regulate which genes are activated or silenced without modifying the DNA sequence, and they play an important role in tumor progression and immune regulation.

In this context, whole-genome bisulfite sequencing (WGBS), ATAC-seq, and Hi-C approaches enable researchers to investigate:

• Altered gene regulation: how DNA methylation, chromatin accessibility, and genome organization affect tumor- and immune-related pathways.
• Cell identity and tumor states: regulatory programs associated with tumor progression, differentiation, and immune cell function.
• Mechanisms of therapy resistance: how epigenetic reprogramming contributes to immune escape and treatment response.

Integrating epigenomic information with genomic and transcriptomic data provides deeper insights into the regulatory mechanisms shaping tumor behavior and immune responses.

3. Adding Spatial Context and Immune Repertoire Information to Understand Tumor–Immune Interactions

The organization of cells within a tumor is critical for understanding cancer progression and immune responses. A cytotoxic T cell located close to tumor cells may have a very different role compared with the same cell type located in a stromal region.

Spatial transcriptomics preserves tissue architecture while profiling gene expression directly within tissue sections, enabling researchers to investigate the localization of tumor and immune populations, cellular interactions, and spatially restricted biological processes.

However, understanding the immune microenvironment requires more than identifying immune cell populations. It also requires understanding their antigen-recognition potential. T cells and B cells recognize tumor antigens through diverse immune receptors generated by V(D)J recombination.

By combining spatial transcriptomics with V(D)J profiling using the BMKMANU S3000 spatial chip, researchers can simultaneously characterize:

• Spatial gene expression: where tumor and immune cells are located and how they interact within the tissue environment.
• Immune repertoire information: which T-cell receptor (TCR) and B-cell receptor (BCR) clones are present and how they are spatially distributed.

This integrated approach enables the study of immune clone expansion, localization of tumor-reactive lymphocytes, and mechanisms underlying immune responses. Instead of viewing immune cells only by their phenotype, researchers can connect their molecular identity, spatial location, and antigen receptor information within the same tissue context.

4. Adding Proteomics and Metabolomics for Functional Insight

While transcriptomic data provide important biological information, RNA levels do not always reflect functional activity. Proteomics adds another molecular layer by directly measuring protein abundance and functional markers involved in tumor–immune communication, including immune signaling pathways and regulatory proteins.

Untargeted metabolomics provides additional insight into the tumor environment by measuring molecules involved in nutrient availability, immune suppression, and cellular metabolism. Tumor cells frequently remodel their metabolic environment to create conditions that suppress immune activity.

By integrating proteomic and metabolomic data with genomic and transcriptomic information, researchers can identify mechanisms of immune escape and potential therapeutic vulnerabilities.

Integrating Multi-Omics Data to Reveal Mechanisms

The power of multi-omics comes from combining multiple biological layers. Together, these approaches generate a comprehensive molecular map of cancer progression and immune response:

• hWGS/WES: Which genomic alterations shape tumor evolution and immune recognition?
• WGBS, ATAC-seq, and Hi-C: Which regulatory mechanisms control tumor and immune cell states?
• Spatial transcriptomics + V(D)J profiling using the S3000 spatial chip: Where are immune cells located, and how do immune clones interact with tumor cells?
• Proteomics + untargeted metabolomics: Which molecular pathways regulate tumor–immune communication and immune escape?

By connecting genomic alterations, epigenetic regulation, spatial organization, immune receptor diversity, protein activity, and metabolic remodeling, multi-omics analysis provides a more integrated framework for studying the tumor immune microenvironment and advancing cancer research.